Reviewed, UniProtKB/Swiss-Prot A1K3U8 (DDL_AZOSB)

Names and origin

Protein names

Recommended name:
    D-alanine--D-alanine ligase
    EC=6.3.2.4
Alternative name(s):
    D-alanylalanine synthetase
    D-Ala-D-Ala ligase

Gene names

Name:	ddl
Ordered Locus Names:	azo0886

Organism

Azoarcus sp. (strain BH72) [Complete proteome] [HAMAP]

Taxonomic identifier

62928 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Betaproteobacteria › Rhodocyclales › Rhodocyclaceae › Azoarcus

Protein attributes

Sequence length	304 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Inferred from homology.

General annotation (Comments)

Function	Cell wall formation By similarity.
Catalytic activity	ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine. HAMAP MF_00047
Cofactor	Binds 2 magnesium or manganese ions per subunit By similarity.
Pathway	Cell wall biogenesis; peptidoglycan biosynthesis. HAMAP MF_00047
Subcellular location	Cytoplasm By similarity.
Sequence similarities	Belongs to the D-alanine--D-alanine ligase family. Contains 1 ATP-grasp domain.

Ontologies

Keywords
Biological process	Cell shape Cell wall biogenesis/degradation Peptidoglycan synthesis
Cellular component	Cytoplasm
Ligand	ATP-binding Magnesium Manganese Metal-binding Nucleotide-binding
Molecular function	Ligase
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	cell wall organization Inferred from electronic annotation. Source: UniProtKB-KW peptidoglycan biosynthetic process Inferred from electronic annotation. Source: HAMAP regulation of cell shape Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cell wall Inferred from electronic annotation. Source: InterPro cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW D-alanine-D-alanine ligase activity Inferred from electronic annotation. Source: HAMAP magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW manganese ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 304	304	D-alanine--D-alanine ligase HAMAP MF_00047		PRO_0000341055
Regions
	Domain	104 – 299	196	ATP-grasp
	Nucleotide binding	130 – 185	56	ATP By similarity
Sites
	Metal binding	253	1	Magnesium or manganese 1 By similarity
	Metal binding	266	1	Magnesium or manganese 1 By similarity
	Metal binding	266	1	Magnesium or manganese 2 By similarity
	Metal binding	268	1	Magnesium or manganese 2 By similarity

Sequences

	Sequence		Length	Mass (Da)
	A1K3U8-1 [UniParc]. Last modified February 6, 2007. Version 1. Checksum: 185E9652BA24A053	FASTA	304	32,635
	10 20 30 40 50 60 MKQRFGKVAV LFGGSSAERD VSLMSGAAVL AALQGAGVDA HAFDPAERDL HILKEEGYDR 70 80 90 100 110 120 VFIALHGRGG EDGTVQGALE LMGIPYTGSG VMASALAMDK WRTKMVWLSC GLPTPRYAIL 130 140 150 160 170 180 DADSDFDAIA RDLGLPIFVK PVHEGSSMGA TKVTEAGQLR AAWELAARYD SLVIAEEFIS 190 200 210 220 230 240 GQELTAPFLD DRALPLVRIV APDGNYDYQH KYFTDDTRYD CPCGLPQAEE EALQALILKS 250 260 270 280 290 300 ARVLGCRGWG RADLILTPEG RPYLLEMNTS PGMTGHSLVP MSARVAGMSF EALCLAILAG ARLG

References

[1]

"Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72." Krause A., Ramakumar A., Bartels D., Battistoni F., Bekel T., Boch J., Boehm M., Friedrich F., Hurek T., Krause L., Linke B., McHardy A.C., Sarkar A., Schneiker S., Syed A.A., Thauer R., Vorhoelter F.-J., Weidner S. , Puehler A., Reinhold-Hurek B., Kaiser O., Goesmann A. Nat. Biotechnol. 24:1385-1391(2006) [PubMed: 17057704] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	AM406670 Genomic DNA. Translation: CAL93503.1.
RefSeq	YP_932390.1.
3D structure databases
ModBase	Search...
Genome annotation databases
GeneID	4609289.
GenomeReviews	Gene locus azo0886 in contig AM406670_GR.
KEGG	azo:azo0886.
Organism-specific databases
CMR	Search...
Phylogenomic databases
OMA	A1K3U8. RAFIILH.
Family and domain databases
HAMAP	MF_00047. [Tree]
InterPro	IPR011761. ATP-grasp. IPR013816. ATP_grasp_subdomain_2. IPR000291. D-Ala_lig_Van_CS. IPR005905. D_ala_D_ala. IPR011095. Dala_Dala_lig_C. IPR011127. Dala_Dala_lig_N. IPR013817. Pre-ATP_grasp. [Graphical view]
Gene3D	G3DSA:3.30.470.20. ATP_grasp_subdomain_2. 1 hit. G3DSA:3.40.50.20. Pre-ATP_grasp. 1 hit.
Pfam	PF07478. Dala_Dala_lig_C. 1 hit. PF01820. Dala_Dala_lig_N. 1 hit. [Graphical view]
TIGRFAMs	TIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITE	PS50975. ATP_GRASP. 1 hit. PS00843. DALA_DALA_LIGASE_1. 1 hit. PS00844. DALA_DALA_LIGASE_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DDL_AZOSB

Accession

Primary (citable) accession number: A1K3U8

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 10, 2008
Last sequence update:	February 6, 2007
Last modified:	June 16, 2009
This is version 23 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)